CysView: protein classification based on cysteine pairing patterns
Identifieur interne : 000112 ( Ncbi/Curation ); précédent : 000111; suivant : 000113CysView: protein classification based on cysteine pairing patterns
Auteurs : Johann Lenffer [Singapour, Australie] ; Paulo Lai [Singapour, Australie] ; Wafaa El Mejaber [Singapour, France] ; Asif M. Khan [Singapour] ; Judice L. Y. Koh [Singapour] ; Paul T. J. Tan [Singapour] ; Seng H. Seah [Singapour] ; Vladimir Brusic [Singapour]Source :
- Nucleic Acids Research [ 0305-1048 ] ; 2004.
Abstract
CysView is a web-based application tool that identifies and classifies proteins according to their disulfide connectivity patterns. It accepts a dataset of annotated protein sequences in various formats and returns a graphical representation of cysteine pairing patterns. CysView displays cysteine patterns for those records in the data with disulfide annotations. It allows the viewing of records grouped by connectivity patterns. CysView's utility as an analysis tool was demonstrated by the rapid and correct classification of scorpion toxin entries from GenPept on the basis of their disulfide pairing patterns. It has proved useful for rapid detection of irrelevant and partial records, or those with incomplete annotations. CysView can be used to support distant homology between proteins. CysView is publicly available at
Url:
DOI: 10.1093/nar/gkh475
PubMed: 15215409
PubMed Central: 441613
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NSW 2006, Australia,</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>School of Molecular and Microbial Biosciences, Building G08, University of Sydney, NSW 2006</wicri:regionArea><orgName type="university">Université de Sydney</orgName><placeName><settlement type="city">Sydney</settlement><region type="état">Nouvelle-Galles du Sud</region></placeName></affiliation></author><author><name sortKey="El Mejaber, Wafaa" sort="El Mejaber, Wafaa" uniqKey="El Mejaber W" first="Wafaa" last="El Mejaber">Wafaa El Mejaber</name><affiliation wicri:level="1"><nlm:aff id="N0x8b519a0.0x9b2ac08">Institute for Infocomm Research, 21 Heng Mui Keng Terrace, 119613 Singapore,</nlm:aff><country xml:lang="fr">Singapour</country><wicri:regionArea>Institute for Infocomm Research, 21 Heng Mui Keng Terrace</wicri:regionArea><wicri:noRegion>21 Heng Mui Keng Terrace</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff wicri:cut=" and" id="N0x8b519a0.0x9b2ac08">IUP Génie Physiologique et Informatique, Bâtiment botanique, 40 av. Recteur Pineau-86022, Poitiers Cedex, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>IUP Génie Physiologique et Informatique, Bâtiment botanique, 40 av. Recteur Pineau-86022, Poitiers Cedex</wicri:regionArea><wicri:noRegion>86022, Poitiers Cedex</wicri:noRegion><wicri:noRegion>86022, Poitiers Cedex</wicri:noRegion></affiliation></author><author><name sortKey="Khan, Asif M" sort="Khan, Asif M" uniqKey="Khan A" first="Asif M." last="Khan">Asif M. Khan</name><affiliation wicri:level="1"><nlm:aff id="N0x8b519a0.0x9b2ac08">Institute for Infocomm Research, 21 Heng Mui Keng Terrace, 119613 Singapore,</nlm:aff><country xml:lang="fr">Singapour</country><wicri:regionArea>Institute for Infocomm Research, 21 Heng Mui Keng Terrace</wicri:regionArea><wicri:noRegion>21 Heng Mui Keng Terrace</wicri:noRegion></affiliation><affiliation><nlm:aff wicri:cut=" and" id="N0x8b519a0.0x9b2ac08">Department of Biochemistry</nlm:aff></affiliation></author><author><name sortKey="Koh, Judice L Y" sort="Koh, Judice L Y" uniqKey="Koh J" first="Judice L. Y." last="Koh">Judice L. Y. Koh</name><affiliation wicri:level="1"><nlm:aff id="N0x8b519a0.0x9b2ac08">Institute for Infocomm Research, 21 Heng Mui Keng Terrace, 119613 Singapore,</nlm:aff><country xml:lang="fr">Singapour</country><wicri:regionArea>Institute for Infocomm Research, 21 Heng Mui Keng Terrace</wicri:regionArea><wicri:noRegion>21 Heng Mui Keng Terrace</wicri:noRegion></affiliation></author><author><name sortKey="Tan, Paul T J" sort="Tan, Paul T J" uniqKey="Tan P" first="Paul T. J." last="Tan">Paul T. J. Tan</name><affiliation wicri:level="1"><nlm:aff id="N0x8b519a0.0x9b2ac08">Institute for Infocomm Research, 21 Heng Mui Keng Terrace, 119613 Singapore,</nlm:aff><country xml:lang="fr">Singapour</country><wicri:regionArea>Institute for Infocomm Research, 21 Heng Mui Keng Terrace</wicri:regionArea><wicri:noRegion>21 Heng Mui Keng Terrace</wicri:noRegion></affiliation><affiliation><nlm:aff wicri:cut=" and" id="N0x8b519a0.0x9b2ac08">Department of Biochemistry</nlm:aff></affiliation></author><author><name sortKey="Seah, Seng H" sort="Seah, Seng H" uniqKey="Seah S" first="Seng H." last="Seah">Seng H. Seah</name><affiliation wicri:level="1"><nlm:aff id="N0x8b519a0.0x9b2ac08">Institute for Infocomm Research, 21 Heng Mui Keng Terrace, 119613 Singapore,</nlm:aff><country xml:lang="fr">Singapour</country><wicri:regionArea>Institute for Infocomm Research, 21 Heng Mui Keng Terrace</wicri:regionArea><wicri:noRegion>21 Heng Mui Keng Terrace</wicri:noRegion></affiliation></author><author><name sortKey="Brusic, Vladimir" sort="Brusic, Vladimir" uniqKey="Brusic V" first="Vladimir" last="Brusic">Vladimir Brusic</name><affiliation wicri:level="1"><nlm:aff id="N0x8b519a0.0x9b2ac08">Institute for Infocomm Research, 21 Heng Mui Keng Terrace, 119613 Singapore,</nlm:aff><country xml:lang="fr">Singapour</country><wicri:regionArea>Institute for Infocomm Research, 21 Heng Mui Keng Terrace</wicri:regionArea><wicri:noRegion>21 Heng Mui Keng Terrace</wicri:noRegion></affiliation><affiliation wicri:level="4"><nlm:aff id="N0x8b519a0.0x9b2ac08">Department of Microbiology, Faculty of Medicine, National University of Singapore, 8 Medical Drive, 117597 Singapore</nlm:aff><country xml:lang="fr">Singapour</country><wicri:regionArea>Department of Microbiology, Faculty of Medicine, National University of Singapore, 8 Medical Drive</wicri:regionArea><orgName type="university">Université nationale de Singapour</orgName></affiliation></author></analytic><series><title level="j">Nucleic Acids Research</title><idno type="ISSN">0305-1048</idno><idno type="eISSN">1362-4962</idno><imprint><date when="2004">2004</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>CysView is a web-based application tool that identifies and classifies proteins according to their disulfide connectivity patterns. It accepts a dataset of annotated protein sequences in various formats and returns a graphical representation of cysteine pairing patterns. CysView displays cysteine patterns for those records in the data with disulfide annotations. It allows the viewing of records grouped by connectivity patterns. CysView's utility as an analysis tool was demonstrated by the rapid and correct classification of scorpion toxin entries from GenPept on the basis of their disulfide pairing patterns. It has proved useful for rapid detection of irrelevant and partial records, or those with incomplete annotations. CysView can be used to support distant homology between proteins. CysView is publicly available at <ext-link ext-link-type="uri" xlink:href="http://research.i2r.a-star.edu.sg/CysView/">http://research.i2r.a-star.edu.sg/CysView/</ext-link>.</p></div></front></TEI></record>Pour manipuler ce document sous Unix (Dilib)
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